/// <summary>
/// add precursor and non-matched annotations
/// </summary>
public override void AddAnnotations(pwiz.MSGraph.MSGraphPane graphPane, Graphics g, pwiz.MSGraph.MSPointList pointList, ZedGraph.GraphObjList annotations)
{
base.AddAnnotations(graphPane, g, pointList, annotations);
//using( Spectrum element = Element )
{
foreach (Precursor p in Element.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
double precursorMz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
int precursorCharge = 0;
CVParam precursorChargeParam = si.cvParam(CVID.MS_charge_state);
if (precursorChargeParam.empty())
{
precursorChargeParam = si.cvParam(CVID.MS_possible_charge_state);
}
if (!precursorChargeParam.empty())
{
precursorCharge = (int)precursorChargeParam.value;
}
double stickLength = 0.1;
ZedGraph.LineObj stickOverlay = new ZedGraph.LineObj(precursorMz, 1, precursorMz, stickLength);
stickOverlay.Location.CoordinateFrame = ZedGraph.CoordType.XScaleYChartFraction;
stickOverlay.Line.Width = 3;
stickOverlay.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
stickOverlay.Line.Color = Color.Green;
annotations.Add(stickOverlay);
// Create a text label from the X data value
string precursorLabel;
if (precursorCharge > 0)
{
precursorLabel = String.Format("{0}\n(+{1} precursor)", precursorMz.ToString("f3"), precursorCharge);
}
else
{
precursorLabel = String.Format("{0}\n(precursor of unknown charge)", precursorMz.ToString("f3"));
}
ZedGraph.TextObj text = new ZedGraph.TextObj(precursorLabel, precursorMz, stickLength,
ZedGraph.CoordType.XScaleYChartFraction, ZedGraph.AlignH.Center, ZedGraph.AlignV.Bottom);
text.ZOrder = ZedGraph.ZOrder.A_InFront;
text.FontSpec.FontColor = stickOverlay.Line.Color;
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
//text.FontSpec.Fill = new Fill( Color.FromArgb( 100, Color.White ) );
text.FontSpec.Angle = 0;
annotations.Add(text);
}
}
}
}
public override Spectrum spectrum(int index, bool getBinaryData)
{
Spectrum s = base.spectrum(index, true);
if (s.cvParam(CVID.MS_MSn_spectrum).empty() ||
(int)s.cvParam(CVID.MS_ms_level).value == 1)
{
if (!getBinaryData)
{
s.binaryDataArrays.Clear();
}
return(s);
}
PrecursorList pl = s.precursors;
BinaryData mzArray = s.getMZArray().data;
BinaryData intensityArray = s.getIntensityArray().data;
PointDataMap <double> mziMap = new PointDataMap <double>();
for (int i = 0; i < (int)s.defaultArrayLength; ++i)
{
mziMap.Insert(mzArray[i], intensityArray[i]);
}
Set <double> pointsToRemove = new Set <double>();
foreach (Precursor p in pl)
{
foreach (SelectedIon si in p.selectedIons)
{
double mz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
PointDataMap <double> .Enumerator itr = mziMap.LowerBound(mz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - mz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
CVParam chargeParam = si.cvParam(CVID.MS_charge_state);
if (!chargeParam.empty())
{
int z = (int)chargeParam.value;
for (int i = 1; i < z; ++i)
{
double strippedMz = (mz * z) / (z - i);
itr = mziMap.LowerBound(strippedMz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - strippedMz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
}
}
}
}
if (getBinaryData)
{
mzArray.Clear();
intensityArray.Clear();
foreach (PointDataMap <double> .MapPair pair in mziMap)
{
if (pointsToRemove.Contains(pair.Key))
{
continue;
}
mzArray.Add(pair.Key);
intensityArray.Add(pair.Value);
}
s.defaultArrayLength = (ulong)mzArray.Count;
}
else
{
s.binaryDataArrays.Clear();
s.defaultArrayLength -= (ulong)pointsToRemove.Count;
}
return(s);
}
public void updateRow(SpectrumDataSet.SpectrumTableRow row, MassSpectrum spectrum)
{
spectrumList[spectrum.Index] = spectrum;
Spectrum s = spectrum.Element; //GetElement(false);
DataProcessing dp = spectrum.DataProcessing;
Scan scan = null;
InstrumentConfiguration ic = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
ic = scan.instrumentConfiguration;
}
if (dp == null)
{
dp = s.dataProcessing;
}
CVParam param;
param = s.cvParam(CVID.MS_ms_level);
row.MsLevel = !param.empty() ? (int)param.value : 0;
param = scan != null?scan.cvParam(CVID.MS_scan_start_time) : new CVParam();
row.ScanTime = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_m_z);
row.BasePeakMz = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_intensity);
row.BasePeakIntensity = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_total_ion_current);
row.TotalIonCurrent = !param.empty() ? (double)param.value : 0;
var precursorInfo = new StringBuilder();
var isolationWindows = new StringBuilder();
if (row.MsLevel == 1 || s.precursors.Count == 0)
{
precursorInfo.Append("n/a");
isolationWindows.Append("n/a");
}
else
{
foreach (Precursor p in s.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
if (precursorInfo.Length > 0)
{
precursorInfo.Append(",");
}
precursorInfo.AppendFormat("{0:G8}", (double)si.cvParam(CVID.MS_selected_ion_m_z).value);
}
var iw = p.isolationWindow;
CVParam isolationTarget = iw.cvParam(CVID.MS_isolation_window_target_m_z);
if (!isolationTarget.empty())
{
double iwMz = (double)isolationTarget.value;
if (isolationWindows.Length > 0)
{
isolationWindows.Append(",");
}
CVParam lowerOffset = iw.cvParam(CVID.MS_isolation_window_lower_offset);
CVParam upperOffset = iw.cvParam(CVID.MS_isolation_window_upper_offset);
if (lowerOffset.empty() || upperOffset.empty())
{
isolationWindows.AppendFormat("{0:G8}", iwMz);
}
else
{
isolationWindows.AppendFormat("[{0:G8}-{1:G8}]", iwMz - (double)lowerOffset.value, iwMz + (double)upperOffset.value);
}
}
}
}
if (precursorInfo.Length == 0)
{
precursorInfo.Append("unknown");
}
row.PrecursorInfo = precursorInfo.ToString();
if (isolationWindows.Length == 0)
{
isolationWindows.Append("unknown");
}
row.IsolationWindows = isolationWindows.ToString();
StringBuilder scanInfo = new StringBuilder();
foreach (Scan scan2 in s.scanList.scans)
{
if (scan2.scanWindows.Count > 0)
{
foreach (ScanWindow sw in scan2.scanWindows)
{
if (scanInfo.Length > 0)
{
scanInfo.Append(",");
}
scanInfo.AppendFormat("[{0:G8}-{1:G8}]",
(double)sw.cvParam(CVID.MS_scan_window_lower_limit).value,
(double)sw.cvParam(CVID.MS_scan_window_upper_limit).value);
}
}
}
if (scanInfo.Length == 0)
{
scanInfo.Append("unknown");
}
row.ScanInfo = scanInfo.ToString();
row.IonMobility = scan != null ? (double)scan.cvParam(CVID.MS_ion_mobility_drift_time).value : 0;
if (row.IonMobility == 0 && scan != null)
{
row.IonMobility = (double)scan.cvParam(CVID.MS_inverse_reduced_ion_mobility).value;
if (row.IonMobility == 0)
{
// Early version of drift time info, before official CV params
var userparam = scan.userParam("drift time");
if (!userparam.empty())
{
row.IonMobility = userparam.timeInSeconds() * 1000.0;
}
}
}
row.SpotId = s.spotID;
row.SpectrumType = s.cvParamChild(CVID.MS_spectrum_type).name;
row.DataPoints = s.defaultArrayLength;
row.IcId = (ic == null || ic.id.Length == 0 ? "unknown" : ic.id);
row.DpId = (dp == null || dp.id.Length == 0 ? "unknown" : dp.id);
}